JAL-1925 update source version in license

[jalview.git] / src / jalview / appletgui / TreeCanvas.java

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 5c62234..47b85d1 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,31 +1,55 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
+import jalview.util.MappingUtils;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.ScrollPane;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class TreeCanvas extends Panel implements MouseListener,
         MouseMotionListener
@@ -578,7 +602,14 @@ public class TreeCanvas extends Panel implements MouseListener,
 
         av.setSelectionGroup(null);
         av.getAlignment().deleteAllGroups();
-        av.sequenceColours = null;
+        av.clearSequenceColours();
+        final AlignViewportI codingComplement = av.getCodingComplement();
+        if (codingComplement != null)
+        {
+          codingComplement.setSelectionGroup(null);
+          codingComplement.getAlignment().deleteAllGroups();
+          codingComplement.clearSequenceColours();
+        }
 
         colourGroups();
 
@@ -636,7 +667,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         if (cs != null)
         {
           cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.getIgnoreGapsConsensus());
+                  av.isIgnoreGapsConsensus());
         }
       }
       // TODO: cs used to be initialized with a sequence collection and
@@ -663,9 +694,31 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       av.getAlignment().addGroup(sg);
 
+      // TODO this is duplicated with gui TreeCanvas - refactor
+      av.getAlignment().addGroup(sg);
+      final AlignViewportI codingComplement = av.getCodingComplement();
+      if (codingComplement != null)
+      {
+        SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+                codingComplement);
+        if (mappedGroup.getSequences().size() > 0)
+        {
+          codingComplement.getAlignment().addGroup(mappedGroup);
+          for (SequenceI seq : mappedGroup.getSequences())
+          {
+            // TODO why does gui require col.brighter() here??
+            codingComplement.setSequenceColour(seq, col);
+          }
+        }
+      }
+
     }
     ap.updateAnnotation();
-
+    if (av.getCodingComplement() != null)
+    {
+      ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
+              "alignment", null, ap.av.getAlignment().getSequences());
+    }
   }
 
   public void setShowDistances(boolean state)